Dark Conversion
by LadyV77
Summary: Complete! A darker spin on the events of Conversion. Spoilers through Conversion, elements of ShWeir. Rating for language, violence and character death.
1. Chapter 1

**Spoilers:** through Season 2 episode "Instinct" (picks up right after it), commercials for "Conversion" and (only slightly) "The Lost Boys"

**Author's Note:** _Italics_ signify thoughts or emphasis. One row of Xs is change of POV, two rows is change of scene.

**Part 1 of 5.**

This is my first attempt at a Stargate: Atlantis fic, so don't be too hard on me.I was challengedto write what I think _could_ happen in the episode "Conversion" in which John Sheppard turns Wraith-buggy, but putting as dark a spin on it as possible (for me, anyway). If you've read anything of mine, you'd know I nearly always write happy fics, so it was quite the challenge (which I _did_ ask for). Also, I am a die-hard ShepWeir shipper, so there will be a little of that reflected in here, though it is by no means a romance.

This was plotted out and mostly written before the actual episode, so it doesn't follow that storyline except for the fact that John is infected and mutating.

**Warnings: **Rating for violence, brief language, and character death. And just because I kill someone off in this fic DOES NOT mean I want them dead on the show.

**Disclaimer:** I don't own Stargate Atlantis or its characters, if I did Elizabeth would go off planet more often, and she and Shep would… well, you can guess. I also don't own a few short lines of dialogue that appeared in the commercial and episode.

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"Colonel Sheppard, you are injured," Teyla remarked when John and Ronon returned to her.

She had felt good enough to sit up only seconds before, and now Teyla allowed herself to be pulled to her feet by Ronon. Her head swam a bit, but she tamped down on the swell of dizziness and concentrated instead on being ready to move back to where Rodney and Carson were waiting with the villagers. She brushed stray bits of the forest floor off her pants and the back of her jacket, picking John's up off the ground where it had served as a cushion for her head. Teyla shook out the cloth, tucking it into the crook of her arm when John showed no inclination to take it back.

"It's just a scratch," John replied, surreptitiously wiping some of the blood off his forearm.

"And Ellia?" Teyla asked with a lift of her brows.

She'd heard the gunfire, and the creature that Ellia had become in her desperation to be human was not with the two men. Teyla's suspicions were confirmed when Ronon and John shared a glance before looking away.

With a soft sigh, she nodded, "I see. We must return to Dr. McKay and Dr. Beckett. The villagers will want to know they no longer have anything to fear from the monster in the forest. I am just relieved that Zaddik did not have to know the fate of his daughter."

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The walk back to where Rodney and Carson waited with the villagers was accomplished quickly and in silence. John was trying to ignore the slight burning sensation in the wound on his arm, thankful that it wasn't worse. He didn't understand why, but Ellia had apparently been unable to feed in the form resulting from Carson's serum. He didn't have a mirror on him, but he knew Ronon or Teyla would have said something if he looked any older or drained in any way.

Perhaps her inability to feed the way the Wraith did was _why_ Ellia had cut into his arm. Maybe she had been trying to latch onto his arm in the way that bug had attached itself to his neck previously. Whatever the reason, Ronon had been right; Ellia had been too far gone, she never would have come back with them. With how many times he and Ronon had been forced to shoot her, John wasn't sure if even a Wraith stun weapon would have been enough.

"The Daemos in the woods will never bother you again," Ronon announced to the villagers when they reached the group.

_Until the next culling_, went unspoken. Why not let the people enjoy their lives while they could?

Sighs of relief and excited chatter followed the announcement, but Carson was not distracted from the fact that one of those under his care had been injured, nor did he forget about the potential use they could get from the deceased Wraith girl's body.

"Colonel, hold still," Carson commanded when John wouldn't let him inspect the wound in his arm. Out of hearing range of the villagers, he remarked, "We have no idea what Ellia could have done to you."

"I'm fine, Beckett," John bit off. "We need to get back to Atlantis and report in."

"What about the body?" Carson asked, finally relenting his hold on John's injured arm. "I need to find out what went wrong, why the serum stripped the human genes instead of those of the Iratus bug."

"We'll send Major Lorne's team back for it," John decided aloud. "Teyla and I are both injured, you and McKay need to carry the equipment back to the 'gate, and I'm pretty sure Ronon would rather have a bonfire with it than carry the body anywhere."

"Aye," Carson replied. "I suppose that's best. Excuse me, Colonel."

The Scottish doctor made his way to Teyla's side to tend to the wound on the back of her head.

The group was back in Atlantis forty minutes later, and John sent a message to Major Lorne to get a team together for the extraction. Elizabeth gasped when she saw the blood seeping through the hastily applied field bandage on his arm, and added her own command to Carson's that the debriefing take place in the medical room.

With her arms crossed, Elizabeth listened to the story of what had happened with Ellia and the stolen test serum. A worried frown remained in place on her face the whole time. While the others took turns with parts of the tale, Carson cleaned and bandaged the cut on the back of Teyla's head before turning his attention once more on John. Rodney and Ronon asked to be excused when their parts in the story had been related, both heading off for a shower, change of clothes and, no doubt, a large meal. John smirked at the thought of the similarities between the otherwise disparate men.

John gritted his teeth when Carson swabbed the wound in his forearm carefully for a DNA sample and scraped a small section of flesh from the area for the same reason. When he had handed them off to a nurse, Carson applied antibiotic cream and bandaged the area.

"Until Major Lorne and the others get back with the body and I run tests on these samples," Carson told Elizabeth, "I won't know the full ramifications of her attack on the Colonel. Teyla needs to stay the night for observation in case of a concussion, and Colonel Sheppard should probably stay as well, just in case."

"Alright," Elizabeth nodded.

"Hold on a minute," John said. "I feel fine. She didn't feed on me." He gestured to his head, "See? No grays."

Carson shook his head, "By the time she attacked you, I don't think Ellia was truly a Wraith any longer. We have no idea what kind of reaction you'll have from the wound, son."

"Look," John made himself say sternly. He really didn't want to stay in medical any longer than he had to. "I'm fine. You said yourself that she was more of an Iratus bug than anything else when she cut me. Once the first bug was off me and you restarted my heart, I didn't suffer any unusual side effects."

Carson didn't have a rebuttal to that, but the worried frown on his face didn't lighten any. Usually that wasn't such a big deal since Carson was always anxious whenever any of the people under his care were sick or injured, but his frown was causing deeper than normal furrows in his forehead. John realized the good doctor was feeling guilty.

"Beckett, you couldn't have known Ellia would do what she did. You were just trying to help."

"John's right, Carson," Elizabeth added. "No one blames you for how this turned out. From what you've all said, Ellia was a very desperate young woman. Now, John, I realize you feel fine now, but I want you to promise me you'll report back to Carson the second you feel at all badly, even if it's just a headache."

In the face of Elizabeth's still very worried expression and Carson's quiet watchfulness, John sighed, "Fine. The second anything bothers me, I'll report back. Can I go now?"

Elizabeth had to stifle a smile at the pleading-little-boy expression he adopted as he had known she would and, after a confirming glance at Carson, she nodded.

It was on the walk to his quarters that John had a horrible thought. When he had been insisting he was fine, he had almost insisted that he felt better than okay, the very same thing Ford had said when he had been injected with an overdose of the Wraith enzyme. Right before he had gone crazy from his addiction to it. Feeling another twinge in his arm, John shook his head at his own thoughts. The wound hurt and he didn't feel like super-anything, so it must just be his conscience hassling him for not being able to spend more time looking for his friend.

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The next day Carson pronounced Teyla clear to leave the medical room. She was sent by the doctor to find John and ask him to check in at some point during the day. John was on his morning run with Ronon when she found him, the taller man a good twenty feet ahead of the Colonel. John jogged to a stop in front of her and smiled.

"Head feelin' better?" he asked.

"Very much, thank you for inquiring," Teyla answered as politely as ever. "Colonel Sheppard, Doctor Beckett would like you to go and see him when you have a free moment."

"Thanks, Teyla." He glanced in the direction Ronon had gone, and shook his head, "If you see Ronon, let him know I cut my run short this morning, will ya?"

Teyla nodded, and John headed in the direction of his room at a brisk walk. Once there, he stripped out of his sweaty clothes and headed for the shower in his in-suite bathroom. Turning the stream of water on to the temperature he liked, John leaned against the sink momentarily to gently peel off the medical tape holding the bandage to his forearm. He tossed it into the garbage before climbing into the shower.

He stood still for long minutes with his head tilted forward, letting the hot water pound on his upper back and shoulders, easing tension and tight muscles that had more to do with stress and worry than anything physical. When John stepped out ten minutes later, he quickly dried himself with a large towel. He hissed in pain when he unthinkingly rubbed his right arm vigorously. Dropping the towel, he stared at the wound on his arm. There were several small lines of blue creating a web-like design expanding from the site.

"Damn it," he swore fiercely.

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Elizabeth entered Carson's office off the infirmary to find Rodney, Teyla and Ronon already there. She took the fourth chair that had been placed in front of Carson's desk, her stomach in knots. The Scot wouldn't have called them all in with John sitting in the infirmary a room away if it was good news. Good news would have been handed directly to John, reported to her and that would be the end of it.

"I'm afraid I have some bad news," Carson unknowingly confirmed Elizabeth's thoughts. "Colonel Sheppard has been infected by a mutated strand of the retrovirus through the wound on his forearm."

Rodney was pale as he rebutted, "Then why isn't he a snarling monster bent on destruction? Ellia was transformed in a matter of minutes."

"Aye, but Ellia, being a Wraith, already had Iratus bug genetics; the Colonel didn't. The tests on the samples I took when we first got back from the planet show a small amount of what the retrovirus became after it had altered Ellia. The Colonel came to me half an hour ago to report that the area around the wound has changed color and texture, the first sign of what I fear will be a transformation much like Ellia's. I've taken more samples, and I suspect they'll show a higher concentration of the retrovirus in the Colonel's blood and tissue."

"You're working on a cure, right?" Elizabeth asked.

Carson flinched. "Aye, lass. I've already got all of my team working on it. I'm afraid I won't know much more until the second round of tests come back."

Ronon's chair suddenly and forcefully scraped backwards making the others cringe at the sound, and the dark man stalked from the room with long strides.

"What was that about?" Rodney asked.

"I believe Ronon is feeling guilty," Teyla answered softly. "Colonel Sheppard ordered Ronon to stay with me when I was injured, and Ronon obeyed the order until I awoke and told him he sometimes must choose to go against orders when he knows they are wrong. Ronon believes if he had been with the Colonel, Ellia would not have been able to attempt to feed on him."


	2. Chapter 2

**Author's Note:** _Italics_ signify thoughts or emphasis. **Part 2 of 5.**

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John picked at a string on the bottom hem of the shirt he was wearing. Luckily, he'd been able to talk Carson out of putting him in a backless gown just for an exam and a few tests. His eyes strayed to the mottled blue skin on his arm and quickly darted away. The dire news Carson had already given him before asking permission to tell Elizabeth and the team flitted through his mind. Okay, so maybe it wasn't _just_ some tests.

It had been more than ten minutes since he had seen Elizabeth join the others in Carson's office. Ronon had been the only one to leave so far, and the Runner had gone straight to the hall without even glancing John's way. Not that John blamed him. Ronon had suffered more than most people in the Pegasus Galaxy did at the hands of the Wraith. Losing his entire planet, having them attempt to feed on him, and then being hunted for sport for seven years, knowing through one mistake that staying even one night with other people would result in more deaths. John didn't know how Ronon had stayed sane. Most people wouldn't have.

And at least John could count on Ronon being able to take the necessary steps without any hesitation if things went horribly wrong.

He looked up as Rodney and Teyla left Carson's office, each of them giving him an encouraging smile, Teyla's more hopeful than Rodney's, before following down the hall in the direction Ronon had gone. Elizabeth exited the room next, alone, but headed straight for him. Just as she reached him, he saw Carson head from his office to the room behind the infirmary John knew the Atlantis doctors used for medical research. It had probably now become the stop-Sheppard-from-turning-Wraith headquarters.

"How are you feeling?" Elizabeth asked, her arms crossed.

John shrugged. "A little wired. The area around the wound is tender, but I don't really feel any different. That almost worries me more than feeling sick would."

"We'll beat this thing," she assured him.

But the way she was holding onto herself told him that she was at least as worried as he was, if not more so.

"You really suck at this whole bedside manner thing," he told her, smiling crookedly to take the sting out of his words.

Elizabeth's stance relaxed a bit as he had hoped it would. She even grinned back at him. Some of the tightness in his chest eased.

"There's a reason I'm a diplomat and not a medical doctor."

"I can tell," he teased. John paused for a moment before adding, "You know Beckett will do everything he can to make sure this thing gets stopped."

"I know," Elizabeth confirmed. "But I'm afraid I'm going to have to take you off active duty for the time being. Carson thinks stress will speed the transformation process. I'm going to have Major Lorne take over your duties unless you have someone else in mind."

John valiantly ignored the sting of not being able to do his job. "Lorne's a good choice. He's a good man, and he respects you and your authority."

_Unlike Caldwell_. The higher ranked CO of the Daedalus wasn't mentioned aloud, but John knew they were both thinking of how much he would enjoy taking advantage of the current situation if he were here for it. Thankfully he wasn't.

When Elizabeth continued to stand beside the bed he was sitting on, looking a bit more lost by the second, John nudged her gently as he stood. "Go on, Elizabeth. If Lorne's going to be taking over for me, you need to keep him updated. Besides, you have a city to run."

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On the fourth day since their encounter with Ellia, John showed up in the room designated for Teyla's stick-fighting sessions as she began a practice session. John was wearing long sleeves to hide the worst of it, but Teyla knew, along with Elizabeth and the other members of Atlantis' flagship team, that his transformation had progressed. The patches of skin that were blue and scaly had increased in number and size, and in some places on his forearms, thorn-like protrusions had begun to form. There were hints of blue skin tone on his face as well, making Teyla wonder how much of his covered skin was getting worse.

"Colonel Sheppard," she greeted. "Is there something I can help you with?"

John lifted the duffle bag in his right hand. Beginning to feel uneasy, Teyla recognized it as the one John kept his own set of sticks in.

"Thought I'd get in some practice since I have the time," he answered.

"I am unsure that is a good idea, Colonel Sheppard. Doctor Beckett said that stress is not good for your condition. I cannot condone participation in something that may cause your condition to worsen."

"Practice isn't stressful," he corrected her. "Sitting around and doing nothing but wait is stressful."

"Very well," Teyla relented. "But it will have to be a short session, or Doctor Beckett will be very angry."

She couldn't help wanting to ease John's boredom. He had done so much for her and her people that she knew she would forever be in his debt. And she could understand his feelings about not being able to do what his job. It was in his nature to protect and he was being forced to go against that.

Teyla had noticed in the many months she had known him that John had a definite childlike side to him. When he liked something, he tended to get very excited over it. It was at odds with his position as a military man and the seriousness with which he undertook his duties, but Teyla thought maybe it was his way of dealing with all of the things he had seen and experienced. To take as much joy as he could where and when he could. When John bounced into position on the mat with a smile, he reinforced Teyla's belief.

A smile briefly touched her own lips as she got into position as well. She decided as she waited that she would let him attack this time instead of defend. He never exerted himself quite as much in offense against her as he did in defending himself, and she still had misgivings about the wisdom of giving into him. It would be best to 'go easy on him' as the Earth saying went.

When the usual allotted time passed and Teyla hadn't moved toward him, John realized what was going on and took up a combat-ready position instead of the defensive one he had been in. A few seconds later he launched himself at her, his sticks coming down hard against hers. Teyla twirled away from him, surprised when he followed closely, more grace evident in his movements than there usually was. As the mock fight progressed, Teyla was forced to switch strategies, defending heavily but occasionally going on the offensive to throw him off a bit. John was doing much better than he usually did.

John executed a move she had used in demonstrations but never actually taught him, and Teyla found herself with both hands, along with the sticks they were holding, trapped above her head. Dropping the weapons so she could get away, she spun closer to him to get out of the hold. She jerked back when her forearm ran against his, a stinging pain telling her that the skin had been broken.

Seeing the pain on her face, John immediately dropped his own sticks and stared in horror at the blood welling from a scratch a few inches long on her arm. It was obvious from the timing and position of the wound that it had been caused by one of the protrusions on his own arm.

"Let's get you to Beckett," John said grimly.

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John paced the part of the infirmary furthest away from Teyla. Carson was in the next room, putting a rush on Teyla's test results. John had apologized to the Athosian woman numerous times in the trip from the gym to the infirmary and she had forgiven him, but John didn't think he could extend himself the same courtesy. Nor could he be that close to her knowing what he might have done.

He had just been so bored cooped up in his room. His first thought had been to go visit with Elizabeth, catch up on all the goings-on in the rest of Atlantis, but then he had caught sight of himself in the mirror. After several minutes of simply staring in shock at how much he had changed, he had realized that everyone he met along the way would look at him the same way, many would react much more negatively. And there were a lot of people between his room and Elizabeth's office.

So he had decided to go see Teyla in the gym where she conducted her stick fighting practices instead. John could get to that part of the city the long way, and the chance of running into someone else would be so much lower. He didn't like taking the coward's way out, but he did anyway. John regretted the choice even more now that Teyla was injured and possibly infected like him. His emotional discomfort was nothing when held up against the health and safety of a member of his team. He didn't know how he would ever forgive himself for this.

Carson emerged and bustled over to Teyla. They spoke briefly and John watched Teyla thank the doctor before leaving the infirmary. John felt a presence beside him and turned to see Elizabeth. She put a gentle hand on his arm, a worried but supportive expression on her face. Carson approached them, urging both of them into his office.

"First of all, you should know that Teyla is going to be just fine," he told them. "There is no sign of the virus in her blood work."

The two leaders of Atlantis sighed in relief almost in unison.

John couldn't help asking, "How is this possible?"

"I'm not entirely sure about the cause, it could be because of your Ancient gene or perhaps because of an unforeseen side effect of your previous encounter with the Iratus bug, but the virus present in your system isn't contagious."

John perked up considerably. "Well, that's good news."

But Carson was still frowning. "Good for Teyla, yes. Not so for you, son."

"What do you mean?" Elizabeth asked before John could, her voice tense.

Carson held up two pieces of paper as visual aids. There were a handful of pictures on both sheets, easily distinguishable as some sort of samples seen under a powerful microscope. Each one was markedly different from the next if one looked close enough to note the details. Carson began pointing to the different squares.

"This is a sample of the original retrovirus. This next one is what it became in Ellia's system. The rest are the different samples I've taken so far from you, Colonel."

"They're all different," John pointed out the obvious. He'd never excelled in sciences that weren't math-based, but he had taken high school biology, and he was sure this wasn't good.

"Aye, they are. The virus is mutating at an astonishing rate. Every time my team thinks of a possible treatment, the virus has already changed so much inside you that it's back to square one. If we don't find some way of slowing it down enough so that we can find a cure…"

"We _will_ find a way," Elizabeth interrupted firmly.

But all John heard was the hopelessness in Carson's voice. When he got back to his room later, he pulled out two sheets of paper and began writing.

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From then on, John stayed in his room except for his check ups with Carson and for meals. He would go to the mess to retrieve his rations and then join Elizabeth in her office. She set the time aside each meal to spend it with only him, but he still had to pass a lot of the populated areas of the city when getting to and from and while getting his food. People stared, some in disgust, most in good old-fashioned horror.

John took to wearing a voluminous cloak with a hood that hid most of his features. On the second day after the close call with Teyla, he had woken to find his eyes had changed to a yellowish green with vertical, slit pupils instead of round ones. He was becoming more alien everyday, and most of the time he avoided mirrors. John glanced at the clock. It was about an hour before the time he usually went to get lunch, but his stomach was growling loudly.

Unable to ignore his hunger anymore, John shrugged into the cloak he had taken to wearing and headed for the door. He almost walked right into it; he was so sure it would open automatically. It always had before. It was a rude awakening to almost smash his nose into the blue-gray structure. He backed away a few steps and walked up to it again. Nothing.

A surge of anger ripped through him, and John used his new claws to get his fingertips into the crack where the two sides of the door met. With a small huff of exertion, he began prying the doors open with his hands. He was almost exultant when the door was open half way. Until he looked up.

Elizabeth stood on the other side of the now open doorway, her mouth hanging open and her small fist raised as if to knock. John blinked at her shocked expression.

"What? It wouldn't open," he said defensively.

Elizabeth found her voice. "I know you're used to Ancient technology automatically working for you, but did you try using the controls?"

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John's jaw tightened and he looked away from her. Elizabeth stepped closer to him with a soft sigh and lightly touched one of his clenched fists. It was hard not to flinch or otherwise react to the scaly texture of his skin, but Elizabeth knew _she_ had to be strong for _him_ for once. When he didn't pull away, she pressed her fingers more firmly around his hand. She was surprised but relieved when his fingers relaxed and turned to wrap her smaller hand in his.

"I'm sorry," he said so low she almost didn't hear him.

Elizabeth squeezed his hand in reply and told him the reason she'd come to see him, "Carson is still working on finding you a cure, but Rodney thinks he's found a way to give him more time."

She didn't add that Carson desperately needed that time, but they both knew it was true. John nodded and pulled the hood of his cloak up over his head. Elizabeth wanted to reach up and pull it off, to show him that she knew it was still him despite the physical changes, but if it helped him feel less exposed and judged, all she could do was let him have the small illusion of anonymity. She shifted her hand in his only enough so that they could walk comfortably. She ignored the looks their joined hands got as they walked the halls, tightening her grip only once when John made a half-hearted attempt to pull away.


	3. Chapter 3

**Author's Note:** _Italics_ signify thoughts or emphasis. **Part 3 of 5.**

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When Elizabeth led him to the lab where months ago they had found her ten thousand year old self, John was relieved and worried at the same time. It would be great if putting him in stasis gave Carson enough time to come up with a treatment or cure, but part of him was terrified of not being aware. What if something happened to the city, to Elizabeth, to everyone? They could be destroyed by the Wraith as he slept and he'd never know it. Would he wake ten thousand years from now to find everything he had ever known gone? But when he glanced at Elizabeth and saw the hope burning in her expressive eyes, he knew he had to let them try it.

Rodney was already in the room, his laptop hooked into the machine's interface. He smiled distractedly at them when they entered the room, gesturing John toward the chamber they'd found the aged Elizabeth Weir in. John pulled off his cloak before getting in, knowing from having fallen asleep with it on once that it wasn't the most comfortable thing to be unconscious in. Rodney gasped but John ignored the sound, knowing it was only shock since Rodney had not seen him quite as… Wraith-buggy… as he was now.

As he climbed into the device and lay back against the smooth, slanted surface, John was disconcerted and yet somehow comforted to find that it still bore Elizabeth's scent. The fact that he could even tell that didn't bother him as much as he thought it would. Heightened senses… it kind of made him feel a bit like the superheroes he had pretended to be while playing as a child.

"We're just going to do a test run first," Rodney commented. "If it works, we'll wake you up and let Carson get some last minute samples and such and let you take care of anything you need to before we put you under more long term."

John nodded his understanding and Rodney turned back to his computer. Elizabeth gave John an encouraging smile that he returned before closing his eyes. Knowing there would soon be a barrier mere inches from his face, John was suddenly glad that he had never been claustrophobic. He sighed softly, wondering if he'd feel anything when the machine activated.

Rodney swore colorfully and started madly tapping on the keys of his laptop. John's eyes flew open and settled on Elizabeth. She was watching Rodney worriedly. Realizing that something wasn't going as planned, John got out of the chamber and approached them, making sure to stay closer to Elizabeth since she wasn't as jumpy about his changed appearance.

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Rodney hung his head in defeat and Elizabeth voiced what they all realized, "It didn't work."

"Of course it didn't work," John scoffed. "Rodney thought of it. I'm surprised it didn't explode and kill us all."

Rodney flinched visibly, and Elizabeth frowned at the infected man, reprimanding, "John!"

He looked at her, his eyebrows raised over his oddly different eyes. It was his 'everyone's thinking it, so I said it' look, but she had never heard him be so deliberately cruel before using it before. At least not to his friends. Elizabeth couldn't think of a way to respond, and John turned and left the lab.

"He's not himself, Rodney," she said when she found her voice.

Rodney shrugged and continued staring at the screen of the laptop attached to the cryogenic chamber's controls, trying to hide how deeply John's comment had cut. Ever since the disaster on Durandan he had been trying to re-prove himself worthy of everyone's faith and trust, John's especially, and he had just failed again. But Elizabeth found it impossible to try to comfort Rodney further when she was still so worried about the bigger problem of John's health. She couldn't help feeling that she, too, was failing the man who had gone to so many extremes so many times to protect her and the other members of the Atlantis expedition.

And she had absolutely no idea what to do about it.

"As far as I can determine," Rodney informed her quietly, "the sensors refused to recognize the Colonel as a human. The Ancients must have built in a failsafe so that the Wraith could never use it. It makes me wonder how different the Wraith hibernation chamber technology is from this."

Elizabeth perked up. "What about that crashed ship you explored a few months ago, the one where you encountered the solitary Wraith? Did it have hibernation chambers? Maybe you could reverse engineer one that would work for him."

"It was just a transport ship, not a full hive ship," Rodney replied despondently. "If it'd had chambers the crew wouldn't have turned on each other for sustenance."

Elizabeth closed her eyes and slowly shook her head. They had come up with only one solution to John's problem, however temporary, and it hadn't worked. She couldn't help but wonder if John now regretted ever choosing to come to Atlantis.

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That evening, Elizabeth was working in her office when someone clearing their throat alerted her to the fact that she had company. She looked up, surprised to see Ronon Dex filling her doorway. He always treated her with respect, probably because John did, but Ronon had never actively sought her out for anything before.

"Can I help you with something, Ronon?" she asked as she waved him into the room.

Teyla entered the room as well. The petite Athosian had been hidden behind the much taller man a moment before.

"Teyla?" Elizabeth added to her question.

"I need to go off world," the man who had rarely said more than one word at a time to her replied.

Teyla huffed softly at his bluntness and attempted to elaborate for him, "Ronon and I went to see Colonel Sheppard earlier. He was quite rude to us, and Ronon took offence. He and Colonel Sheppard almost came to blows."

Elizabeth sighed and leaned back heavily in her chair. She knew from the latest mission report that Ronon was blindly hateful of the Wraith, not that she could blame him with what he had been through. But the current situation must be difficult for him to deal with. Everyone had seen the respect and loyalty he gave John, and now John was turning, more or less, into a Wraith.

"And you're afraid if you are confronted with each other again while he is in this condition that one of you may end up hurting the other?"

Ronon nodded once to show that Elizabeth had guessed correctly. "I also have something to take care of."

"To show that he has every intention of coming back and keeping his word to keep the city of the Ancestors a secret, Ronon has asked that I join him if you allow him to leave Atlantis," Teyla informed her. "And I have agreed."

"Very well," Elizabeth conceded. "But be careful."

"Thank you, Dr. Weir," Teyla responded.

Ronon added an appreciative grunt to the end of their conversation.

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Three days later, the alarm sounded for an unscheduled incoming wormhole.

"Shield up," Elizabeth told the man at the control panel.

She waited tiredly, knowing she didn't have the energy or the heart to deal with another crisis on top of the one that was now getting worse by the hour instead of by the day. Morale was at an all-time low with the military leader of the city not expected to recover and the flagship team no longer together. Elizabeth could only be thankful that Colonel Caldwell was safely out of the way in the Milky Way galaxy picking up more supplies and personnel. If she had to deal with him on top of everything else and he made one of his usual snide remarks about John, she would have gladly shot him right between his smug, squinty little eyes. And not with a stunner.

"It's Teyla's IDC, ma'am," the man at the 'gate controls reported.

"Open it."

With a flash, the shield disintegrated from the surface of the event horizon. Moments later Ronon stepped through, a body slung over one broad shoulder. Teyla followed, keeping a Wraith stun weapon trained on the figure being carried by her companion. Ronon turned to say something to Teyla, and Elizabeth got a better view of his captive from her balcony. It was the long-missing Lieutenant Aidan Ford.

Her eyes wide, Elizabeth ordered the nearest military officer to get a team down to the 'gate room immediately. She left the balcony and control room area quickly to move down to the 'gate room herself.

"What…" she trailed off, unsure what exactly she'd meant to ask.

"I made a promise to Sheppard to get his friend back for him," Ronon said gruffly. "I keep my promises."

He didn't add 'before it was too late' but they both knew that was a large part of why he'd found it necessary to go looking for Ford now when he hadn't in the weeks since joining up with them.

"How did you find him?" Elizabeth asked.

"Wasn't hard since we weren't recognizable to his scouts as being from Atlantis," Ronon replied. "He was recruiting those hit hardest by the Wraith to join in his fight against them. Promising to help make them as strong as he is."

"Perhaps it would be best to continue this conversation once Lieutenant Ford is safely secured," Teyla remarked.

Though the Athosian still had the stun weapon trained steadily on the young man she had considered her friend, Elizabeth could now see in the other woman's eyes how nervous she was. There must have been quite a fight between Ronon and Ford. Elizabeth nodded in response to Teyla's comment and led the way to the holding cell that had been home so far to two Wraith. It felt wrong to put one of their own in it after it had been occupied by 'Steve' and 'Bob,' but Elizabeth had to acknowledge it was probably the only way they could hold him until Carson could find a way to free Ford of his addiction to the Wraith enzyme.

Ronon set his burden on the floor of the cell and stepped back beside Elizabeth. The energy shielding around the cell was activated. Elizabeth ordered a full guard detail on Ford, with her being their first notification when he woke. She left to head for John's room, hoping the news would raise his spirits a bit.

When she reached it, however, the guard positioned outside his room told her he was sleeping. Disappointed that she couldn't cheer him up with the news yet, Elizabeth went to her office to work on some of the paperwork she had fallen so behind on the last several days. Less than an hour later her earpiece crackled to life, a frantic voice telling her that Lieutenant Ford had escaped when Dr. Beckett, believing Ford to still be unconscious, had entered the cell to take a blood sample. Dr. Beckett was being treated for a broken arm and one of the guards for contusions and a possible concussion.

Right after that, the guard from John's room contacted her to let her know that the Colonel had left his room in the direction of the 'gate room at a dead run. His guard had been unable to keep up but he was on his way.

Elizabeth got out from behind her desk and exited into the control room, only to find Grodin's replacement and the rest of the staff slowly backing out of the room, a crazed-looking Ford waving a gun at them. John entered the doorway on the far side of the room a moment after everyone else was gone. Ford stilled and simply stared at the changes in his former CO.

Even Elizabeth was surprised at the severity of John's condition. He had been avoiding contact with her the past couple days since the failed attempt at putting him in stasis, but she hadn't fully realized what the passing time meant to his status. Or maybe she just hadn't wanted to. The blue, mottled skin had spread, what she could see of his arms no longer held any hint of human flesh tone, and the color on his neck had spread to also cover most of the lower half of his face. There were hints of the color on his forehead and the area around his yellow-green eyes. The spines and ridges on his arms were more pronounced and there was evidence of more of them growing in on his jaw line.

"What the hell happened to Sheppard?" Ford yelled when he got over his shock. His gaze spun in an arc around the room, landing on Elizabeth. "_You_ let this happen to him."

He stalked toward her, the weapon he had undoubtedly stolen from one of the guards pointed directly at her head. Elizabeth was frozen, knowing from what the others had told her and what she had observed of his behavior that Ford was not going to listen to reason. In fact, she might very well make it worse if she didn't keep her mouth shut.

Elizabeth was unable to prevent the gasp from escaping her mouth when the blurred form of her mutating second-in-command moved between she and Ford. "John!"

Surprised by the lightning fast move, Ford's hand jerked, pulling the trigger of his stolen gun. The bullet struck John's shoulder and Elizabeth let out a small shriek, but John barely flinched. He reached behind him with the same arm, and when his hand motioned her to come closer, she obeyed, keeping herself nearly pressed against his back as he warily edged around Ford. Elizabeth wasn't sure if he was trying to find the best route of escape or the best way to attack Ford. The only thing she knew for sure was that she trusted the mutating man with her life much more than the younger one who was now clearly off his rocker. Actually, the same most likely would have been true even if Ford had been completely normal.

"Mine," John growled warningly to Ford when the younger man tried to train his gun once more on Elizabeth.

Ford looked surprised for only a moment before the frown on his face deepened, "Get out of the way, Sheppard. I don't want to go through you to get to her, but I will if I have to."

Elizabeth stumbled when her hip struck the corner of a desk, and Ford made his move. He darted to the side so that John was no longer between Ford's gun and his target. Fortunately, John was faster. Elizabeth watched in a mixture of horror and relief as John snapped Ford's neck before the enzyme-addicted young man even knew what hit him.

John was breathing hard as Ford's body slipped to the floor. Major Lorne appeared at the doorway, taking in the situation with a quick glance.

"Shut down the alarm," he said over the comm in his ear. "And call off the search, Lieutenant Ford has been found and neutralized."

Elizabeth was still watching John, who was switching his gaze between her and the man in the doorway. He was still wary, holding his body tensely.

Lorne took a step toward Elizabeth, asking, "Are you alright, ma'am?"

With a feral snarl, John leapt across the room, once more putting Elizabeth behind him. Major Lorne raised his weapon quickly, training it on John's chest. Elizabeth roused herself from her shock enough to find her voice.

"Stand down, Major," she ordered as calmly as she could. "Back away slowly."

Lorne frowned but followed orders, lowering his weapon... though Elizabeth could tell from his stance that it would be raised and used in a matter of seconds if he thought it necessary to protect her. After an obvious hesitation, he backed toward the doorway he had come through. John reacted, straightening from the slight crouch he had been in and reaching out to touch her, as if to reassure himself that she was there.

"I'm okay," she told both men. To Lorne she said, "I think it would be best if I led the Colonel back to his room. He's much more likely to remain calm that way."

"Yes, ma'am," Lorne responded, ordering the other guards out in the hallway to stand down and clear the way.

Elizabeth gently grasped John's hand, hoping she was right and that he would let her lead him back to his room. Though he kept his eyes on Major Lorne, John did allow her to guide him. It was a slow process, Major Lorne walking backwards about fifteen feet in front of them, clearing hallways as they went so no one would cause a reaction in the still agitated Colonel. When they reached his room and Elizabeth opened his door using the control panel beside it, John tugged her forward into the room with him.

Major Lorne raised his weapon again, but Elizabeth said, "It's alright. He just wants to know I'm safe. When he calms down, I'll come out."

"Ma'am…" Lorne tried.

"Major, if I need you, you'll know it, trust me."

"Yes, ma'am," he agreed reluctantly as he watched the door slowly slide shut between them.


	4. Chapter 4

**Author's Note:** _Italics_ signify thoughts or emphasis. **Part 4 of 5.**

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John backed her into a corner and eased her down so she was sitting on the floor before pacing the perimeter of the room. Elizabeth stayed still and watched his movements, recognizing that he was making sure they were safe from further threats. She just hoped the guards stayed far enough from the door that they wouldn't make him more agitated. Right now she didn't think John considered anyone other than her a non-threat.

After five minutes, John was apparently somewhat mollified and returned to her side. He settled into a crouch beside her, his arm brushing hers. Elizabeth waited patiently until his stance had relaxed further.

"John?" He tilted his head in her direction without looking at her and she continued, "I'm okay now. We both are."

He looked at her then, and though his eyes were even more non-human than they had been mere days ago, the gaze was still somehow John's.

"Hurt you?"

The words were stilted and rough, but Elizabeth knew what he was asking. "No, John, he didn't hurt me. You stopped him." A shiver wracked her body. "He won't ever hurt anyone again."

"Killed Ford." The words sounded choked, and Elizabeth thought guilt was creeping in now that the danger had passed. But John kept speaking. "Had to. Stop hurting… protect."

John was struggling to speak, and Elizabeth asked gently for clarification, "Stop Ford from hurting me? Protect me?"

He nodded once, firmly, and settled more fully beside her.

"Safe," he grunted.

"We're all safe now, John," she told him. "Thanks to you. But I have to go back out there and let everyone else know we're okay."

He immediately tensed. "No."

"I have to." Elizabeth reminded him, "It's my job."

"No," he said again, moving to stand over her, a dark look on his face.

_Oh, boy_, Elizabeth thought. _I should have known it wouldn't be that easy_.

Something she couldn't hear caught John's attention and after a 'stay there' glance at her, he moved to the door of the room. He crouched close to it, listening intently from what Elizabeth could tell, a waiting stillness in his stance.

The wireless headset in her ear… that she had, quite frankly, forgotten in the commotion and subsequent worry… crackled to life, quieter than normal. Elizabeth darted a glance at John, but he was still intent on the door.

"Can you hear me, lass?" She barely made out Carson's voice. "Major Lorne was worried that the Colonel might not let you go, and it has been several minutes. Rodney turned the headset connection down as far as he dared, and he and the Major are providing a distraction. If you answer aloud the Colonel is sure to notice that you're not talking to him, so just press the call button once for no and twice for yes. Alright?"

Taking care that her movements weren't too sudden, Elizabeth eased her right hand up to ear level, shifting so it appeared she was leaning on that arm, and pressed the small button on the device in her ear twice.

"Good," Carson answered. "Now, has he hurt you at all?"

One immediate and emphatic depression of the knob.

Elizabeth heard Carson sigh with relief before continuing. "Is he by the door now?"

Two clicks.

"Will he let you leave the room?"

One click.

"Alright, we have a plan to get you out without risking harm to you, the Colonel or anyone else, but it will require you to get close to the Colonel. Can you without risk to yourself?"

Two clicks.

"Good. We'll clear everyone away from the door and leave a food try outside it. Rodney will open the door remotely, and hopefully Colonel Sheppard will take the tray inside for the two of you. Hidden in the napkin will be a powerful sedative. You'll have to administer it, lass. Once he's out, call us on the headset. Can you do that?"

Two clicks.

"Alright. If at anytime you feel that you're in danger, let us know and we'll come in and get you out by force. It'll be just a few moments before the plan starts. Beckett out."

At any other time, Elizabeth would have laughed at the relatively mild-mannered and definitely non-military Carson using that phraseology, but she knew he only did it so she would know he wasn't waiting for an answer. Apparently the distraction had stopped, because John's stance relaxed. He had just turned to move back to her side when the door slid open soundlessly. John spun, ready to pounce, but the only thing visible in the open doorway was a tray with more than enough food for two people.

John cautiously stuck his head out of the door and looked around briefly before picking up the tray. As soon as he had moved back into the room, the door slid shut again. He gave the door a dirty look but continued on to Elizabeth's corner of the room, setting the tray down in front of her. John squatted across the tray from her, nudging it gently in her direction when she simply waited.

Given the all clear, Elizabeth looked over the available fare, taking note of the turkey sandwiches, John's favorite, and the empty glasses among other items. She lifted the glassware and held them out to John.

"Could you get us some water?"

He blinked, his head tilted slightly, but took the two tumblers, turning toward the in-suite bathroom. By sheer luck or perhaps some tactical design of John's, Elizabeth's corner was across the room from the bathroom. As soon as he started walking that direction, Elizabeth lifted the napkin closest to her to find it empty. She quickly switched the napkins and discovered a small vial of powder in the second one.

Lifting the top slice of bread from the sandwich nearest John's side of the tray, Elizabeth dusted the sedative onto the mayonnaise present there. She mentally crossed her fingers, hoping his taste buds weren't heightened like the rest of his senses, at least enough that he wouldn't be able to taste the drug. John returned shortly thereafter, handing her one of the glasses of water before settling on the floor to sit across from her.

Twenty minutes after John had finished eating and five minutes after she had polished off half of what he'd left her, the sedative started taking effect. His eyes began drifting, the lids drooping heavily. John's head started nodding, and he shook himself in an effort to snap out of the daze.

"John," Elizabeth called to him gently. "Why don't you lay down and get some sleep?"

He shot her a look that clearly told her he didn't want to leave her unguarded. Making a snap decision, Elizabeth straightened her legs and patted her lap with one hand. John simply stared at her for a full minute before an all-too-human sigh escaped between his blue lips. He dragged himself sluggishly to her side, showing her just how strong the sedative had been. His eyes closed the moment his head touched her lap.

Elizabeth laid her left hand on his shoulder and gently stroked his messy, bed head hair with her right. She waited three minutes after the last of the tension left his body before raising her hand to her headset and quietly calling Carson in.

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Major Lorne and an additional six members of the military contingent escorted Carson into the room. The CMO could see the heartache visible on Elizabeth's face, but the fact that she didn't protest the heavy guard told him more about John's condition than Major Lorne's report that the Colonel had killed Lieutenant Ford.

Carson hadn't wanted to believe it, but when he examined the body he was forced to admit to himself that only the mutating Colonel could have gotten close enough fast enough to snap the enzyme-addicted young man's neck. Well, perhaps Ronon could have as well, but Ronon and Teyla had both been with him in the infirmary for just-back-from-off-world check-ups when it had happened.

The other men surged forward to surround the unconscious Colonel. Elizabeth took off her jacket and made a bundle of it, easing it under John's head as she slipped her leg out from beneath his head. Major Lorne pulled her to her feet, asking quietly if she was alright. Elizabeth nodded and stood back when Carson approached to take a new blood sample and use one of the Ancient scanning devices.

When Carson was done, Lorne asked, "Should we move him to the cell, ma'am?"

Elizabeth shook her head, "No, we'll just keep him locked in here. I think it will be safer that way. But we will need more men on guard duty. How many Wraith stunners were we able to salvage from the siege of the city?"

"Nearly four dozen," Lorne answered.

"Good. Arm the guards with them," she ordered. Done with the Major, Elizabeth turned to Carson. "I'll be waiting in my office when you get the results of the most recent tests."

Carson nodded, watching with a worried expression as the leader of the Atlantis expedition left the room, moving with less grace and energy than she usually conveyed.

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"What did you find?" Elizabeth asked as soon as Carson sat across from her.

The Scot looked as exhausted and worn down as she felt, but she couldn't stop hoping that _someone_ would have good news for her eventually.

"The scan I did shows further build up of the hard tissues that manifest as the ridges and spines on his skin. There's also evidence of pinchers like the Iratus bug's coming in."

Elizabeth sank back in her chair, hanging her head. John would look even less human very soon.

"I also did a complete workup on the latest blood sample."

"And?" she prompted.

Carson sighed. "He has very little human DNA left, there's even less in him than in the various Wraith I've examined samples of."

"What does that mean, Carson?" Elizabeth asked, fearing she already knew the answer and not truly wanting to hear it.

"I'm sorry, lass," he answered, not meeting her eyes. "There's nothing I or anyone else can do for him."


	5. Chapter 5

**Author's Note:** _Italics_ signify thoughts or emphasis. **Part 5 of 5.**

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Elizabeth stood in her office, trying to think of what could possibly be done. Trying being the operative word. Her brain refused to work. She had been standing in the same place for nearly an hour. She knew her chair was right behind her; it had been pressing against the backs of her knees the whole time. But somehow she couldn't force herself to sit down.

She couldn't sit at her desk in her office, reports piled in front of her, and pretend this was just another problem. She couldn't deal with this, because then she'd have to deal with being alone. With the fact that she had lost more than a second in command. As much as John had been on this expedition in the first place by sheer random genetics and then thrust into a position of command by the untimely death of another, he had given more than his all, more than anyone should be expected to give.

At every turn he had gone beyond the call of duty, calling on reserves no ordinary man possessed in order to keep Atlantis and its people… and her… safe. They sometimes disagreed and argued over the way to do certain things, but they respected each other's opinions. She knew with him that he listened to her, not merely nodding absently while planning his own moves like other military personnel she'd had experience with. He supported, protected and encouraged her. And he had become the best friend she'd ever had. More than that…

"Dr. Weir!" a voice crackled on her headset.

Snapped out of her thoughts, Elizabeth responded, "Yes, Sergeant Matthews?"

The sick feeling in the pit of her stomach intensified. Matthews had been left in charge of the men on guard duty.

"Ma'am, Colonel Sheppard has escaped his quarters. He broke out through one of the windows. As far as we can tell, he climbed along the outer wall to an uninhabited room a few doors down. Ellison was stationed down the hall and tried to stop the Colonel, but he… Ellison's dead, ma'am, and two others are seriously injured. Beckett's on his way."

"Stay with the injured men, Sergeant. Major Lorne will take things from here."

"Yes, ma'am. The Major has been updated as well."

"Thank you, Sergeant."

Elizabeth sat abruptly. She lowered her head, burying her face in her hands momentarily. This was her fault. She should've had him transferred to the holding cell after he killed Ford protecting her. Her refusal to give up hope that John would be okay had now resulted in the loss of an innocent life. Knowing she'd have the rest of her life for self-recriminations and guilt, Elizabeth put the steel back in her spine.

"Any indication of where he's headed?" she asked over her headset.

Major Lorne's voice responded after a crackle, "We believe the 'gate room, ma'am."

"Follow at a safe distance and tell me if he changes direction," she ordered before leaving her office for the control room. "Give me citywide." She waited until receiving a confirming nod from the man at the main console. "Attention Atlantis, this is Dr. Weir. Colonel Sheppard has escaped and is making his way to the 'gate room from the residential corridors. Please stay inside whatever rooms you are in with the doors locked and keep the halls clear. We don't want any unnecessary confrontations. I will give the all clear as soon as possible. Thank you."

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Ronon made his way to Elizabeth's office as soon as she made her citywide announcement. She was standing behind her desk with her arms loosely crossed over her stomach, her hands wrapped around herself. Her face was sad and thoughtful. Ronon cleared his throat to get her attention.

"What are you going to do?" he asked when she looked up at him.

"I don't know," she admittedly quietly.

Ronon shifted uncomfortably, aware of the closeness between Elizabeth and John through his observation of their interactions even if he was not sure of its full context. But he couldn't let what Elizabeth might be feeling stop him from saying what needed to be said. He was a very practical person when it came to survival; seven years running from the Wraith tended to do that to a person. And maybe she needed him to say it since no one else was going to.

"You only have three options," he ventured.

Elizabeth's eyebrows drew together, "You thought of a whole three? I haven't been able to come up with anything at all."

"You can keep him locked up in that holding cell for the rest of his life, send him to an uninhabited planet through the Stargate, or kill him." Elizabeth flinched, but Ronon pressed on. "If you choose either of the first two options and he ends up needing to feed like the Wraith or those bugs, you'll be condemning him to a slow, painful death through starvation."

Elizabeth was silent for long minutes, jumping slightly when one of her underlings stuck his head in for a moment to tell them that Colonel Sheppard had entered the 'gate room. She squeezed her eyes shut tightly, swiping away the single tear that escaped to trail down her right cheek before looking back up at Ronon.

"Would you…" she trailed off.

Ronon nodded tersely and turned to head for the stairs that led down to the floor of the 'gate room.

"Ronon," Elizabeth called. He turned his head. "Make it as quick as possible."

He nodded his head once in acknowledgment.

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Elizabeth forced herself to follow Ronon out and move to her oversee-the-returnees spot to watch. She hugged her arms to her stomach tightly, reminding herself that he was no longer John. And even if a tiny piece of him still was, the part that had protected her from all threats, this was a more humane ending than any of their other choices. It was what John would have wanted.

After a first… _last_ look at John, her eyes trailed Ronon as he slowly moved toward the mutated Colonel. It was over quickly, just as she had asked; Ronon using what she assumed was his weapon's highest setting in three quick, successive bursts. Elizabeth felt every shot as if they were hitting her, a small part of her dying inside as the being that had once been John Sheppard fell for the last time.

A fist had closed around her heart when right before he had turned to watch Ronon approach, John had looked up at her like he always did before and after off-world missions. She had to keep reminding herself that very little had been left of the real him, and within days, or even hours, there would have been nothing of John Sheppard but a new, very dangerous species.

Elizabeth sent a subdued message to Carson to come get the body before telling one of the civilians in the room that she was leaving him in charge until her next shift. Elizabeth took the comm device out of her ear and left it on the closest desk.

She had someone to say goodbye to.

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The broken window in John's room had already been covered up with what look like the top panel of a packing crate when Elizabeth got there. The violated glass was the only thing that showed any hint of what the room's inhabitant had become. That and her jacket at the base of one wall, as if it had been thrown against it. Had he felt betrayed waking up to find her gone? Was he even capable of feeling betrayal at that point?

Everything else was much like it had been every other time she had been in his room. The bed was made with military precision, and though some things weren't put away, the room felt lived in rather than messy. Elizabeth wandered aimlessly through John's possessions, trailing a hand over different things. He'd managed to smuggle in more of his things when they'd come back from Earth on the Daedalus, as each of them had.

A small smile of remembrance lifted the corners of her mouth as she passed the long board leaning against one wall. When things had calmed down after the storm during which Kolya and his Genii invasion team had tried to take Atlantis, John had told her that he had never seen waves that big. That any surfer would have given his or her right arm to be able to explore all the beaches of the mainland directly after the storm had passed. John, of course, had been too busy with his duties to take advantage of the change in surf, but he'd promised in passing to teach her how if they ever both had downtime when they could get way from the city.

Her heart squeezed painfully as Elizabeth wondered if there ever would have been such a time if he had survived the infection. She moved away from the board, heading with watery eyes for the bed. She sat quietly for several minutes until the tears that had threatened were under control.

'War and Peace' sat on the nightstand, the bookmark indicating John's progress not even close to a quarter of the way through. She reached for the book absently, letting out a small gasp when a paper wedged underneath it fell to the floor.

Elizabeth leaned forward to retrieve the folded sheet, the tears welling once more in her eyes when she saw her name written in John's masculine scrawl. There were two pages folded together, and Elizabeth opened them, careful not to let her falling tears mar the paper.

_Elizabeth,_

_I'm writing this now, when all that has changed is some of how I look and a bit of an increase in strength, so that it is done for later when I no longer have the mental faculties to be able to do it. I know you still hope that Carson will find his miracle cure, but I've accepted that it's already too late. No matter what happens, I know you'll do the right thing. I have no right to ask any of this of you, but I hope that what we might have…would have shared if things had continued to progress is as clear to you as it is to me. If our positions had been reversed, which I never would have wanted, you know I would have taken care of everything for you._

_Please apologize to anyone I might have hurt. Let the people who are important to me know that I wish them the best. When Carson's done with my body, remind him it isn't his fault, and then cremate me. I'd like my ashes dropped off our balcony where the older you was let go. Send one of my tags back to Earth, to the Air Force, as is called for by procedure, but I'd like you to keep the second one if you feel comfortable doing so. I'd also like you to have anything else of mine you'd like to keep. Hey, maybe you'd like my room; it is bigger than yours. I suppose under the circumstances I shouldn't tell you that the thought of you sleeping in my bed makes me smile, but it does._

Elizabeth couldn't help the small grin that broke through her tears. It was such a John thing to say. She could picture the playful smirk that would have been curving his lips as he wrote it.

_My biggest fear now is that everyone will remember what I became instead of who I was. I take comfort in the knowledge that I know that isn't true of you. I think a part of me, the best part, will live on in your heart. Coming to Atlantis may have been a fluke of genetics, but it became home… my city. General O'Neill once told me that he thought anyone who didn't want to step through the Stargate to different worlds was insane. I feel the same way about anyone who would say no to the adventure of life in the Pegasus Galaxy. When I think about all the things I wouldn't have seen and done and learned if I hadn't taken that risk… not the least of which was getting the chance to know and work with you… I know I made the right choice, despite how it ended for me. _

_I hope they send you someone who unlike Caldwell actually has a beating heart, who cares more about the people in his command than the position he has, but even if you get stuck with him, I know you'll keep him in line. Look at what you were able to accomplish with a maverick like me beside you. You're a great leader, Elizabeth, and I want you to always remember that. Never let anyone forget the importance of this expedition. But most of all, don't forget to take the time to appreciate the wonder of all you see and do and try to think of me in those moments._

_Yours forever,_

_John_

The sheet of paper that followed the letter was a dry list of his last wishes, signed 'Lt. Colonel John Sheppard.' The letter was just for her, the list a way to let her follow his requests without anyone else intruding into this last private thing between them. There would be talk when she kept one of his tags and moved into his room, keeping most of his things, but he was gone and no matter what anyone said or how they felt about the situation, John was no longer here.

Neither one of them would be replaced because of their feelings. And Elizabeth would hold onto these last pieces of him with all her strength. She would need the connection to him to make it through the coming years and be able to make the right decisions for their city. The word love had never been mentioned by either of them, but Elizabeth knew it was what he was referring to in his letter. She knew that even though she hadn't said it, he had known how she felt. He hadn't wanted to sully the emotion by simply writing it, and in a way she was grateful for that.

With a heartfelt sigh, Elizabeth folded the letter and put it back under 'War and Peace' for later. She stood, the list clutched in her hands, ready for her to begin implementing his wishes. Elizabeth cast a quick glance around. She would be back, and soon, but this was the last time it would be anything but her room.

"Goodbye, John," she whispered.

**The End.**


End file.
